Neurons communicate through the formation of specialised junctions termed synapses, established by formation of extended protein networks. Our aim is to gain insights about the protein environment of the synapse by identification of novel proteins through employment of unbiased quantitative proteomic approaches. Here, we show results from a proteomic analysis of synaptic CAH10 protein complexes, which were affinity isolated from mouse brain. CAH10 was recently described as a pan-neurexin ligand. The interactome of CAH10 consists of presynaptic, secreted and post-synaptic proteins. Among them, the multi-pass membrane protein XKR6 was identified. XKR6 belongs to a poorly characterised protein family called X Kell blood group related. Recent studies indicated, that these proteins, as shown for XKR8, might act as phospholipid scramblases. Although, mutations in XKR6 were linked to various neurological disorders, the function of neuronal XKR6 is largely unclear. Affinity purifications of XKR6 complexes from mouse brain derived membranes and AAV- infected hippocampal neurons driving overexpression of XKR6 were performed and coupled with nano-LC MS\MS analysis for identification and quantification of interacting proteins. As a result, XKR6 interacts with a set of synaptic and axonal related proteins. In line with these findings, immunostainings for XKR6 in neuronal cultures correlate with a localisation in axons and the active zones of presynapses. Synaptic characterisations upon knockdown of XKR6 in hippocampal cultures suggest that XKR6 is not important for the formation of synapses. Our results for the first time shed light on the role of neuronal XKR6, a protein linked to the McLeod neuroacanthocytosis syndrome.